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author | BioArchLinuxBot | 2023-06-01 21:03:52 +0000 |
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committer | BioArchLinuxBot | 2023-06-01 21:03:52 +0000 |
commit | f87a93a8f4fa1bbc50bdfdb0ef5a9efca6a47a5d (patch) | |
tree | 93d7da88da9d290828b863b832412647e4bfbcbd | |
parent | 19f3c3d1d0772abad9e993b27e59f53bd4a478b8 (diff) | |
download | aur-f87a93a8f4fa1bbc50bdfdb0ef5a9efca6a47a5d.tar.gz |
[lilac] updated to 2.2.2.20190706.162801-2
-rw-r--r-- | .AURINFO | 16 | ||||
-rw-r--r-- | .SRCINFO | 33 | ||||
-rw-r--r-- | PKGBUILD | 71 |
3 files changed, 55 insertions, 65 deletions
diff --git a/.AURINFO b/.AURINFO deleted file mode 100644 index a4cf8ab5ecf1..000000000000 --- a/.AURINFO +++ /dev/null @@ -1,16 +0,0 @@ -pkgbase = cufflinks - pkgdesc = Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.. - pkgver = 2.2.1 - pkgrel = 1 - url = http://cufflinks.cbcb.umd.edu - arch = x86_64 - license = Artistic - depends = boost - depends = eigen3 - depends = python2 - depends = samtools - depends = perl - source = http://cufflinks.cbcb.umd.edu/downloads/cufflinks-2.2.1.tar.gz - -pkgname = cufflinks - @@ -1,17 +1,24 @@ pkgbase = cufflinks - pkgdesc = Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.. - pkgver = 2.2.1 - pkgrel = 5 - url = http://cole-trapnell-lab.github.io/projects/cufflinks/ + pkgdesc = Transcriptome assembly and differential expression analysis for RNA-Seq. + pkgver = 2.2.2.20190706.162801 + pkgrel = 2 + url = http://cole-trapnell-lab.github.io/cufflinks/ arch = x86_64 - license = Artistic - depends = boost - depends = eigen3 - depends = python2 - depends = samtools - depends = perl - source = https://github.com/cole-trapnell-lab/cufflinks/archive/v2.2.1.tar.gz - md5sums = 80328ff4169f2778c0728a4795da85e2 + license = BSL + makedepends = autoconf + makedepends = make + makedepends = ncurses + makedepends = boost + makedepends = eigen + makedepends = git + makedepends = samtools + makedepends = htslib + depends = python + depends = htslib + depends = boost-libs + source = git+https://github.com/cole-trapnell-lab/cufflinks.git + source = cufflinks.patch::https://github.com/cole-trapnell-lab/cufflinks/pull/108.patch + sha1sums = SKIP + sha1sums = 081021851cfcc0372bcf1f2e56aa11d0a3b5862c pkgname = cufflinks - @@ -1,49 +1,48 @@ -# Maintainer: Grey Christoforo <first name @ last name .net> +# Maintainer: Guoyi Zhang <myname at malacology dot net> +# Contributor: Charles E. Vejnar <ce@vejnar.org> pkgname=cufflinks -pkgver=2.2.1 -pkgrel=5 -pkgdesc="Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.." +_realname=cufflinks +pkgver=2.2.2.20190706.162801 +pkgrel=2 +pkgdesc="Transcriptome assembly and differential expression analysis for RNA-Seq." +url="http://cole-trapnell-lab.github.io/cufflinks/" arch=("x86_64") -url="http://cole-trapnell-lab.github.io/projects/cufflinks/" -license=('Artistic') -depends=('boost' 'eigen3' 'python2' 'samtools' 'perl') -source=(https://github.com/cole-trapnell-lab/${pkgname}/archive/v${pkgver}.tar.gz) -md5sums=('80328ff4169f2778c0728a4795da85e2') +license=("BSL") +depends=('python' 'htslib' 'boost-libs') +makedepends=('autoconf' 'make' 'ncurses' 'boost' 'eigen' 'git' 'samtools' 'htslib') +source=("git+https://github.com/cole-trapnell-lab/cufflinks.git" + "$pkgname.patch::https://github.com/cole-trapnell-lab/cufflinks/pull/108.patch") +sha1sums=('SKIP' + '081021851cfcc0372bcf1f2e56aa11d0a3b5862c') +pkgver () { + cd "$srcdir/$pkgname" + printf "$(cat configure.ac | grep 'AC_INIT' | sed "s@\[@@g;s@\]@@g;s@,@@g" | awk '{print $2}').%s" "$(TZ=UTC git log -1 --pretty='%cd' --date=format-local:%Y%m%d.%H%M%S)" +} prepare() { - cd $srcdir/$pkgname-$pkgver - - sed -i 's,hash\[pos\]\.hash,(hash[pos].hash),g' src/GHash.hh - - curl -L https://github.com/cole-trapnell-lab/cufflinks/commit/305ee7ba4fa8e8df095d293b9e0827c6a85679a8.patch | patch -p1 - curl -L https://github.com/cole-trapnell-lab/cufflinks/commit/6c62baa6a9f3a00b71c8fc8f7f4059a7fe49824.patch | patch -p1 - - curl -L https://github.com/cole-trapnell-lab/cufflinks/pull/87/commits/b7313fffc9d1e3dc92ce8a90b0dd5b2e16cfd68f.patch | patch -p1 - - #curl -L https://github.com/cole-trapnell-lab/cufflinks/pull/108/commits/d1fdcfd1441d1a8c3b5ecaa1b60a4ae876350061.patch | patch -p1 - #curl -L https://github.com/cole-trapnell-lab/cufflinks/pull/108/commits/80219fc315208adb4941a20701d68c25f56db756.patch | patch -p1 - - curl -L https://github.com/cole-trapnell-lab/cufflinks/pull/107/commits/7aa2922ab1f4ff600bd6854cdebb4be6d3b06fa5.patch | patch -p1 - - ./autogen.sh - # cufflinks uses python2 but archlinux uses python3 as default python - perl -i -pne '$_ =~ s/python/python2/ if $_ =~ /^#!\/usr/' src/cuffmerge - - export EIGEN_CPPFLAGS="-I/usr/include/eigen3" - export LDFLAGS="-L/usr/lib -lboost_system" - ./configure --prefix=/usr + cd $srcdir/$pkgname +# for 2.2.1 +# sed -i "16d" configure.ac +# sed -i "s@bam/sam.h@htslib/sam.h@g" src/hits.h +# sed -i "s@boost/tr1/unordered_map.hpp@boost/unordered_map.hpp@g" src/biascorrection.h + sed -i "17d" configure.ac + sed -i "s@sprintf((char \*)vdptr(vs),cmdline);@sprintf((char \*)vdptr(vs),\"%s\",cmdline);@g" src/locfit/makecmd.c + sed -i "s@int curwin;@extern int curwin;@g" src/locfit/startlf.c + patch -p1 < $srcdir/$pkgname.patch } build() { - cd $srcdir/$pkgname-$pkgver - export EIGEN_CPPFLAGS="-I/usr/include/eigen3" - export LDFLAGS="-L/usr/lib -lboost_system" - make + cd $srcdir/$pkgname + autoreconf --install + ./configure --prefix=/usr --with-boost --with-eigen --with-bam \ + LIBS="-lboost_system -lboost_thread -lboost_serialization" + make CXXFLAGS="-I/usr/include/eigen3 -I/usr/include/htslib/ -std=c++11 -lhts -lpthread" } package() { - cd "$srcdir/$pkgname-$pkgver" - make DESTDIR="$pkgdir/" install + cd "$srcdir/$pkgname" + make install DESTDIR="$pkgdir" + install -Dm 644 LICENSE $pkgdir/usr/share/licenses/$pkgname/LICENSE } |